Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring—Ruan-2022

Environmental DNA (eDNA) combined with metabarcoding is an useful approach for assessing species composition and richness in aquatic habitats and is increasingly used to analyze fish variety. No eDNA-based protocol to monitor fish diversity has been established. We tested two filtering procedures and three DNA extraction methods using three filtration water volumes to establish an appropriate approach for eDNA-based fish diversity monitoring in the Pearl River Estuary (PRE), a highly anthropogenically damaged estuary ecosystem. Direct filtering was better for PRE eDNA metabarcoding than filtration-based precipitation. DNeasy Blood and Tissue Kit (BT) and classic phenol/chloroform (PC) extraction produced larger DNA yields, amplicon sequence variants (ASVs), and Shannon diversity indices, and more homogeneous and consistent community composition among repetitions. PC and BT techniques had better species detection, fish variety, and consistency than other combined protocols for 1000 and 2000 mL filtration volumes, respectively. All PRE eDNA metabarcoding processes were more sensitive than bottom trawling, and combining the two techniques increased taxonomic diversity. Combining traditional and eDNA approaches improved accuracy. These results suggest that fish community monitoring in estuarine habitats should use eDNA metabarcoding with caution.

Ruan HT, Wang RL, Li HT, Liu L, Kuang TX, Li M, Zou KS. Effects of sampling strategies and DNA extraction methods on eDNA metabarcoding: A case study of estuarine fish diversity monitoring. Zool Res. 2022 Mar 18;43(2):192-204. doi: 10.24272/j.issn.2095-8137.2021.331. PMID: 35084125; PMCID: PMC8920846.